Sun Oct 9 11:36:04 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:36:04 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6512156 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 28.10400 75.28000 ymin,ymax (A): 11.56500 66.23200 zmin,zma (A): 57.51800 99.00900 x,y,z range (A): 47.17600 54.66700 41.49100 scale (grids/A): 0.6512156 object centre (A): 51.69200 38.89850 78.26350 number of atom coordinates read : 2032 total number of charged atoms : 1968 net assigned charge : -0.4999951 assigned positive charge : 299.6927 centred at (gu) : 89.15280 90.13834 89.27467 assigned negative charge : -300.1933 centred at (gu) : 89.05758 90.10268 89.35424 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6153 nv = 96 ne = 84 npr = 39221 no. pairs analyzed = 39221 no. exposed pairs = 2860 no. arc points = 19580 no. surface atoms = 961 nbur = 1071 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 353 mr = 3214 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0115012E-08 -9.1962482E-09 midg,1,midg; midg,igrid,midg -5.1666245E-09 3.4640419E-09 1,midg,midg; igrid,midg,midg -1.5209709E-08 8.7609076E-09 gauss-seidel spectral radius is 0.9877404 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 11:36:05 rms-change max change #iterations 0.1321026 21.11874 at 10iterations 1.3222850E-02 1.936458 at 20iterations 1.3783398E-03 0.3057556 at 30iterations 1.3761007E-04 2.0622253E-02 at 40iterations 1.4354269E-05 2.1820068E-03 at 50iterations finished qdiffx linear iterations at : 11:36:08 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 1.4354269E-05 2.1820068E-03 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 11:36:08 3.698u 0.192s 0:04.27 90.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:36:08 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.953647 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 28.10400 75.28000 ymin,ymax (A): 11.56500 66.23200 zmin,zma (A): 57.51800 99.00900 x,y,z range (A): 47.17600 54.66700 41.49100 scale (grids/A): 1.953647 object centre (A): 51.69200 38.89850 78.26350 number of atom coordinates read : 2032 total number of charged atoms : 1968 net assigned charge : -0.4999951 assigned positive charge : 299.6927 centred at (gu) : 87.45825 90.41478 87.82372 assigned negative charge : -300.1933 centred at (gu) : 87.17265 90.30818 88.06282 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 65842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19580 grid for indexing accessible points = 1.400000 m= 24552 mr = 44864 m= 4369 mr = 17589 m= 306 mr = 2749 m= 4 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 29788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 15556 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6512156 object centre at (A) : 51.69200 38.89850 78.26350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2965690E-03 -4.7781989E-03 midg,1,midg; midg,igrid,midg -1.9563217E-02 -2.2056943E-02 1,midg,midg; igrid,midg,midg -9.7793564E-03 1.4841123E-02 gauss-seidel spectral radius is 0.9986600 estimated iterations to convergence 216 setup time was (sec) 0.5600000 now iterating at: 11:36:09 rms-change max change #iterations 3.807327 166.6249 at 10iterations 1.790364 81.30858 at 20iterations 0.8411212 27.27567 at 30iterations 0.3980801 12.94618 at 40iterations 0.1879477 6.869002 at 50iterations 8.8391580E-02 3.051235 at 60iterations 4.1676939E-02 1.365889 at 70iterations 1.9663533E-02 0.7068007 at 80iterations 9.2423419E-03 0.3051453 at 90iterations 4.3871626E-03 0.1529846 at 100iterations 2.0560052E-03 6.5464944E-02 at 110iterations 9.7222294E-04 3.4078598E-02 at 120iterations finished qdiffx linear iterations at : 11:36:17 total time elapsed so far: 8.380000 # loops : 120 mean,max change (kT/e) : 9.7222294E-04 3.4078598E-02 energy calculations done at 8.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.520000 DelPhi exited at 11:36:17 8.519u 0.209s 0:09.12 95.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 11:36:17 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.930470 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 28.10400 75.28000 ymin,ymax (A): 11.56500 66.23200 zmin,zma (A): 57.51800 99.00900 x,y,z range (A): 47.17600 54.66700 41.49100 scale (grids/A): 2.930470 object centre (A): 51.69200 38.89850 78.26350 number of atom coordinates read : 2032 total number of charged atoms : 1968 net assigned charge : -0.4999951 assigned positive charge : 299.6927 centred at (gu) : 86.18722 90.62221 86.73553 assigned negative charge : -300.1933 centred at (gu) : 85.75910 90.46238 87.09428 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 152384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19580 grid for indexing accessible points = 1.400000 m= 76646 mr = 108947 m= 29996 mr = 61559 m= 8103 mr = 23941 m= 1216 mr = 5992 m= 65 mr = 782 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 67170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 15744 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.953647 object centre at (A) : 51.69200 38.89850 78.26350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1288918 -4.8395335E-03 midg,1,midg; midg,igrid,midg -0.1770298 -0.4024035 1,midg,midg; igrid,midg,midg -0.1890274 9.8061204E-02 gauss-seidel spectral radius is 0.9992663 estimated iterations to convergence 291 setup time was (sec) 1.180000 now iterating at: 11:36:19 rms-change max change #iterations 9.119130 406.5461 at 10iterations 5.391579 140.5668 at 20iterations 3.167243 73.17964 at 30iterations 1.853939 42.74944 at 40iterations 1.082069 23.41993 at 50iterations 0.6298472 13.62331 at 60iterations 0.3663788 7.826417 at 70iterations 0.2121022 4.123789 at 80iterations 0.1227902 2.284714 at 90iterations 7.0923559E-02 1.448089 at 100iterations 4.1050527E-02 0.8519669 at 110iterations 2.3709100E-02 0.4880934 at 120iterations 1.3677369E-02 0.2533140 at 130iterations 7.9028159E-03 0.1629615 at 140iterations 4.5656790E-03 8.4370613E-02 at 150iterations 2.6243844E-03 4.5961380E-02 at 160iterations 1.5147333E-03 2.8642654E-02 at 170iterations 8.7230146E-04 1.7475605E-02 at 180iterations finished qdiffx linear iterations at : 11:36:32 total time elapsed so far: 13.58000 # loops : 180 mean,max change (kT/e) : 8.7230146E-04 1.7475605E-02 energy calculations done at 13.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.73000 DelPhi exited at 11:36:32 13.728u 0.261s 0:14.56 96.0% 0+0k 0+0io 0pf+0w